Purpose:

To determine the DGE profiles (for human, HBV and HDV genes), relative to uninfected controls, of self-assembling co-cultures of primary human hepatocytes (SACC-PHHs) mono-infected with HBV or co-infected with HBV/HDV at 8 and 28 days post-infection. This run includes the samples sequenced in July 2018.

library(dplyr)
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library(stringr)
library(ggplot2)
library(reshape2)
library(DESeq2)
## Loading required package: S4Vectors
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library(dplyr)
library(RColorBrewer)
library(stringr)
library(genefilter)
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library(genefilter)
library(ggrepel)
library(viridis)
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source("http://bioconductor.org/biocLite.R")
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biocLite("org.Hs.eg.db")
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require(org.Hs.eg.db)
## Loading required package: org.Hs.eg.db
## Loading required package: AnnotationDbi
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## Attaching package: 'AnnotationDbi'
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##     select
## 

Function to perform DGE analysis with both donor and treatment set as factors influencing the counts.

DGE_analysis <- function(sampledirectory) {
a <- basename(Sys.glob(file.path(sampledirectory, "*.txt")))
sample_names <- sub('.txt', '', a)
##Here the donors are renamed based off the Hurel names (i.e. HU___) - RNASeq reads were all 
##named using a different ID system.
sampleTable <- data.frame(sampleName = sample_names, sampleFile = a, treatment = 
    ifelse(grepl("Ctrl", a), "mock", ifelse(grepl("*co|*HDV", a),"coinf", "HBV")), 
   donor = ifelse(grepl("BD330*", a), "HU1019", 
                  ifelse(grepl("BD405*", a), "HU1020", 
                            ifelse(grepl("HU1016*", a), "HU1016", "HU1007"))),
   time = ifelse(grepl("*D8|Day 8", a), "d8", "d28"), 
   replicate = ifelse(grepl("*sample_1h|*D8_ah|*D8_aa|*D8_am|*sample_1m", a), "a",
          ifelse(grepl("*sample_2h|D28_bh|D28_ba|D28_bm|*sample_2m", a), "b", 
           ifelse(grepl("*sample_3h| * sample 1h|* sample 1m", a), "c",
            ifelse(grepl("* sample 2h|* sample 2m", a), "d",
             ifelse(grepl("* sample 3h|* sample 3m", a), "e", ""))))))
dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = sampledirectory, 
                                  design = ~donor + treatment)
dds
dds@colData
contrast <- c("treatment", levels(sampleTable$treatment))
output_basename <- sprintf("%s-%s_vs_%s_%s_analysis", "HumanHBVgenes", contrast[2], 
                           contrast[3], levels(sampleTable$time))
output_basename
dds <- estimateSizeFactors(dds)
dds@colData
dds <- estimateDispersions(dds)

plotDispEsts(dds, main=sprintf("%s Dispersion Estimates", output_basename))
dds <- nbinomWaldTest(dds)
res <- results(dds, contrast=contrast)
res <- res[order(res$padj, -abs(res$log2FoldChange)),]
mcols(res, use.names=TRUE)
##Log-intensity ratios = M values, log-intensity averages = A values
##Red points indicate padj < 0.1. 
plotMA(res, alpha=0.1, main=sprintf(output_basename))
attr(res, "filterThreshold")

metadata(res)$alpha
metadata(res)$filterThreshold
plot(metadata(res)$filterNumRej,
     type="b", ylab="number of rejections",
     xlab="quantiles of filter")
lines(metadata(res)$lo.fit, col="red")
abline(v=metadata(res)$filterTheta)

key = "ENSEMBL"
cols = c("ENTREZID", "SYMBOL", "GENENAME", "ALIAS", "REFSEQ", "ACCNUM")
for (col in cols) {
  # Get annotation data for column
  annotation_data <- AnnotationDbi::select(org.Hs.eg.db, rownames(res), col, keytype=key)
  # Collapse one-to-many relationships
  tmp <- aggregate(annotation_data[col], by=annotation_data[key],
                   # to a list
                   FUN=function(x)list(x))
  # Match on key and append to results
  idx <- match(rownames(res), tmp[[key]])
  res[[col]] <- tmp[idx,col]
}

output_data <- as.data.frame(res)
LIST_COLS <- sapply(output_data, is.list)
for (COL in colnames(output_data)[LIST_COLS]) {
  output_data[COL] <-
    sapply(output_data[COL],
           function(x)sapply(x, function(y) paste(unlist(y),
                                                  collapse=", ") ) )
}

# Save data frame above as tab-separated file
write.table(output_data,
            file=file.path("Human DGEs_donortreatment", paste(Sys.Date(), 
            "human_donor_treatment",output_basename, "_results.txt", sep='')), 
            quote=FALSE, sep="\t", row.names=TRUE, col.names=NA)
return(list(dds@colData, head(res)))
}


##For each timepoint, determine the DGE profile when comparing the different treatments 
##groups to one another (i.e. HBV-infected versus control).

##uninfected control cells versus those mono-infected with HBV
DGE_analysis("Human d8_ctrlvHBV")
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates

## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns

## [[1]]
## DataFrame with 12 rows and 5 columns
##                               treatment    donor     time replicate
##                                <factor> <factor> <factor>  <factor>
## BD330_Ctrl_D8humanHBVgenes         mock   HU1019       d8          
## BD330_HBV_D8humanHBVgenes           HBV   HU1019       d8          
## BD405A_Ctrl_D8humanHBVgenes        mock   HU1020       d8          
## BD405A_HBV_D8humanHBVgenes          HBV   HU1020       d8          
## Ctrl_D8_sample_1humanHBVgenes      mock   HU1007       d8         a
## ...                                 ...      ...      ...       ...
## HBV_D8_sample_1humanHBVgenes        HBV   HU1007       d8         a
## HBV_D8_sample_2humanHBVgenes        HBV   HU1007       d8         b
## HBV_D8_sample_3humanHBVgenes        HBV   HU1007       d8         c
## HU1016 Ctrl D8humanHBVgenes        mock   HU1016       d8          
## HU1016_B_D8humanHBVgenes            HBV   HU1016       d8          
##                                      sizeFactor
##                                       <numeric>
## BD330_Ctrl_D8humanHBVgenes     0.81649517899625
## BD330_HBV_D8humanHBVgenes     0.722206297298348
## BD405A_Ctrl_D8humanHBVgenes   0.535544074331218
## BD405A_HBV_D8humanHBVgenes    0.510842004431757
## Ctrl_D8_sample_1humanHBVgenes   1.8560572037995
## ...                                         ...
## HBV_D8_sample_1humanHBVgenes   1.56574934988419
## HBV_D8_sample_2humanHBVgenes   1.10877923024603
## HBV_D8_sample_3humanHBVgenes   1.52270712654435
## HU1016 Ctrl D8humanHBVgenes   0.889277023545197
## HU1016_B_D8humanHBVgenes      0.523762795147403
## 
## [[2]]
## log2 fold change (MLE): treatment HBV vs mock 
## Wald test p-value: treatment HBV vs mock 
## DataFrame with 6 rows and 12 columns
##                         baseMean    log2FoldChange             lfcSE
##                        <numeric>         <numeric>         <numeric>
## AAB59969.1      2072.96301802315  10.4400443686251 0.452981751652525
## AAB59970.1      1565.31811760815  9.87162678928923 0.611933183516194
## AAB59972.1      190.005850792109  10.6311053508616 0.871839060142464
## AAB59971.1      161.867877694322  10.2941275823554 0.874365749561944
## ENSG00000187498    658.350424669 -1.50677233404892 0.191146706436798
## ENSG00000137801 1726.61042238045 -1.52493760532793 0.244484553722964
##                              stat                pvalue
##                         <numeric>             <numeric>
## AAB59969.1       23.0473839852019 1.56249540527572e-117
## AAB59970.1       16.1318703662489  1.52336244902277e-58
## AAB59972.1       12.1938851295839  3.35058197897517e-34
## AAB59971.1       11.7732511680755  5.36175411706471e-32
## ENSG00000187498 -7.88280563205583  3.20110807387631e-15
## ENSG00000137801 -6.23735766577673  4.45023705734201e-10
##                                  padj ENTREZID SYMBOL
##                             <numeric>   <list> <list>
## AAB59969.1      2.31389944567282e-113       NA     NA
## AAB59970.1       1.12797372537891e-54       NA     NA
## AAB59972.1       1.65395895088811e-30       NA     NA
## AAB59971.1       1.98505541799028e-28       NA     NA
## ENSG00000187498  9.48104189320685e-12     1282 COL4A1
## ENSG00000137801  1.09839267636963e-06     7057  THBS1
##                                       GENENAME
##                                         <list>
## AAB59969.1                                  NA
## AAB59970.1                                  NA
## AAB59972.1                                  NA
## AAB59971.1                                  NA
## ENSG00000187498 collagen type IV alpha 1 chain
## ENSG00000137801               thrombospondin 1
##                                                                ALIAS
##                                                               <list>
## AAB59969.1                                                        NA
## AAB59970.1                                                        NA
## AAB59972.1                                                        NA
## AAB59971.1                                                        NA
## ENSG00000187498                         c("BSVD", "RATOR", "COL4A1")
## ENSG00000137801 c("THBS", "THBS-1", "TSP", "TSP-1", "TSP1", "THBS1")
##                                                                                                      REFSEQ
##                                                                                                      <list>
## AAB59969.1                                                                                               NA
## AAB59970.1                                                                                               NA
## AAB59972.1                                                                                               NA
## AAB59971.1                                                                                               NA
## ENSG00000187498 c("NM_001303110", "NM_001845", "NP_001290039", "NP_001836", "XM_011521048", "XP_011519350")
## ENSG00000137801                                 c("NM_003246", "NP_003237", "XM_011521971", "XP_011520273")
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ACCNUM
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                <list>
## AAB59969.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         NA
## AAB59970.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         NA
## AAB59972.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         NA
## AAB59971.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         NA
## ENSG00000187498                                         c("AA678474", "AAA52006", "AAA52042", "AAA53098", "AAF72630", "AAH47305", "AAI42627", "AAI51221", "AAK53382", "AAK92480", "AAM97359", "AAP43112", "AB209646", "ABE73157", "ABX47006", "AF258349", "AF363672", "AF400431", "AF536207", "AH002650", "AY285780", "BAD92883", "BC047305", "BC142626", "BC151220", "BU677787", "CAA29075", "CAA31276", "CAA68698", "CD613007", "CN256264", "DQ464183", "EAX09108", "EAX09109", "EU260121", "H40591", "M11315", "NM_001303110", "NM_001845", "NP_001290039", "NP_001836", "P02462", \n"X03963", "X05561", "XM_011521048", "XP_011519350", "Y00706")
## ENSG00000137801 c("AAA21126", "AAA21127", "AAA36741", "AAA61178", "AAA61237", "AAB59366", "AAH28145", "AAI36470", "AAI36471", "AB209912", "AI147670", "AI168683", "AI290070", "AK291639", "AK293230", "AK304754", "AK309613", "AK310820", "AU117102", "AU279999", "BAD93149", "BAF84328", "BAG56769", "BAG65509", "BC015134", "BC028145", "BC136469", "BC136470", "BG115371", "BG251169", "BM512145", "BM784452", "BU676185", "CA411820", "CAA28370", "CAA32889", "CEF49520", "EAW92379", "EAW92380", "EAW92381", "LN607833", "M14326", \n"M25631", "M99425", "NM_003246", "NP_003237", "P07996", "X04665", "X14787", "XM_011521971", "XP_011520273")
DGE_analysis("Human d28_ctrlvHBV")
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates

## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns

## [[1]]
## DataFrame with 12 rows and 5 columns
##                                treatment    donor     time replicate
##                                 <factor> <factor> <factor>  <factor>
## BD330_Ctrl_D28humanHBVgenes         mock   HU1019      d28          
## BD330_HBV_D28humanHBVgenes           HBV   HU1019      d28          
## BD405A_Ctrl_D28humanHBVgenes        mock   HU1020      d28          
## BD405A_HBV_D28humanHBVgenes          HBV   HU1020      d28          
## Ctrl_D28_sample_1humanHBVgenes      mock   HU1007      d28         a
## ...                                  ...      ...      ...       ...
## HBV_D28_sample_1humanHBVgenes        HBV   HU1007      d28         a
## HBV_D28_sample_2humanHBVgenes        HBV   HU1007      d28         b
## HBV_D28_sample_3humanHBVgenes        HBV   HU1007      d28         c
## HU1016 Ctrl D28humanHBVgenes        mock   HU1016      d28          
## HU1016_B_D28humanHBVgenes            HBV   HU1016      d28          
##                                       sizeFactor
##                                        <numeric>
## BD330_Ctrl_D28humanHBVgenes    0.736034904845711
## BD330_HBV_D28humanHBVgenes      1.33827133500969
## BD405A_Ctrl_D28humanHBVgenes   0.438063892537815
## BD405A_HBV_D28humanHBVgenes     0.29006208835542
## Ctrl_D28_sample_1humanHBVgenes  2.33170342720659
## ...                                          ...
## HBV_D28_sample_1humanHBVgenes   1.25484305155098
## HBV_D28_sample_2humanHBVgenes   1.67942007539527
## HBV_D28_sample_3humanHBVgenes   1.34803238058423
## HU1016 Ctrl D28humanHBVgenes   0.494723596467327
## HU1016_B_D28humanHBVgenes      0.461540433802861
## 
## [[2]]
## log2 fold change (MLE): treatment HBV vs mock 
## Wald test p-value: treatment HBV vs mock 
## DataFrame with 6 rows and 12 columns
##                         baseMean   log2FoldChange             lfcSE
##                        <numeric>        <numeric>         <numeric>
## AAB59969.1      1918.35454687059 8.88481993959276 0.339851221207296
## AAB59970.1      1556.99540930345 9.97502386577637 0.698181168571559
## AAB59972.1      172.626838978635 8.02490706391143  0.70802645868014
## AAB59971.1      115.521935885071 7.91293964574011 0.781597160225105
## ENSG00000183607 11.6836956046813 23.5901376915131  3.05874798852879
## ENSG00000134193 13.8351447468139 23.5071411915572  3.05867581138834
##                             stat                pvalue
##                        <numeric>             <numeric>
## AAB59969.1      26.1432632433396 1.17564477956107e-150
## AAB59970.1      14.2871568509714  2.63134746813491e-46
## AAB59972.1      11.3341909268066  8.88493579500364e-30
## AAB59971.1      10.1240639659708  4.32093131007735e-24
## ENSG00000183607 7.71235086381195  1.23520981758647e-14
## ENSG00000134193 7.68539807456329  1.52521994765974e-14
##                                  padj ENTREZID SYMBOL
##                             <numeric>   <list> <list>
## AAB59969.1      1.99906638316564e-146       NA     NA
## AAB59970.1        2.2371716174083e-42       NA     NA
## AAB59972.1       5.03598160860807e-26       NA     NA
## AAB59971.1       1.83682789991388e-20       NA     NA
## ENSG00000183607  4.20070154764808e-11   200504   GKN2
## ENSG00000134193  4.32247333166769e-11    83998   REG4
##                                     GENENAME
##                                       <list>
## AAB59969.1                                NA
## AAB59970.1                                NA
## AAB59972.1                                NA
## AAB59971.1                                NA
## ENSG00000183607                 gastrokine 2
## ENSG00000134193 regenerating family member 4
##                                                                      ALIAS
##                                                                     <list>
## AAB59969.1                                                              NA
## AAB59970.1                                                              NA
## AAB59972.1                                                              NA
## AAB59971.1                                                              NA
## ENSG00000183607 c("BRICD1B", "GDDR", "PRO813", "TFIZ1", "VLTI465", "GKN2")
## ENSG00000134193                        c("GISP", "REG-IV", "RELP", "REG4")
##                                                                                                      REFSEQ
##                                                                                                      <list>
## AAB59969.1                                                                                               NA
## AAB59970.1                                                                                               NA
## AAB59972.1                                                                                               NA
## AAB59971.1                                                                                               NA
## ENSG00000183607                                                                 c("NM_182536", "NP_872342")
## ENSG00000134193 c("NM_001159352", "NM_001159353", "NM_032044", "NP_001152824", "NP_001152825", "NP_114433")
##                                                                                                                                                                                                                                                                                                                                                                            ACCNUM
##                                                                                                                                                                                                                                                                                                                                                                            <list>
## AAB59969.1                                                                                                                                                                                                                                                                                                                                                                     NA
## AAB59970.1                                                                                                                                                                                                                                                                                                                                                                     NA
## AAB59972.1                                                                                                                                                                                                                                                                                                                                                                     NA
## AAB59971.1                                                                                                                                                                                                                                                                                                                                                                     NA
## ENSG00000183607                                                                                                                                                                                                     c("AAO85515", "AAQ89027", "AAY24521", "AF494509", "AJ966788", "AY358664", "AY943908", "BC110809", "CAI85014", "EAW99860", "NM_182536", "NP_872342", "Q86XP6")
## ENSG00000134193 c("AAG02562", "AAH17089", "AAK48435", "AAK59869", "AAM95598", "AAM95599", "AAM95600", "AF254415", "AF345934", "AK057107", "AY007243", "AY126670", "AY126671", "AY126672", "BC017089", "BF242936", "CAK22302", "EAW56711", "EAW56712", "EAW56713", "EAW56714", "NM_001159352", "NM_001159353", "NM_032044", "NP_001152824", "NP_001152825", "NP_114433", "Q9BYZ8")
##uninfected control cells versus those co-infected with HBV and HDV
DGE_analysis("Human d8_ctrlvcoinf")
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates

## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns

## [[1]]
## DataFrame with 16 rows and 5 columns
##                                           treatment    donor     time
##                                            <factor> <factor> <factor>
## BD330 HBV_HDV Day 8 sample 1humanHBVgenes     coinf   HU1019       d8
## BD330 HBV_HDV Day 8 sample 2humanHBVgenes     coinf   HU1019       d8
## BD330 HBV_HDV Day 8 sample 3humanHBVgenes     coinf   HU1019       d8
## BD330_Ctrl_D8humanHBVgenes                     mock   HU1019       d8
## BD330_HBV_HDV_D8_ahumanHBVgenes               coinf   HU1019       d8
## ...                                             ...      ...      ...
## Ctrl_D8_sample_1humanHBVgenes                  mock   HU1007       d8
## Ctrl_D8_sample_2humanHBVgenes                  mock   HU1007       d8
## Ctrl_D8_sample_3humanHBVgenes                  mock   HU1007       d8
## HU1016 Ctrl D8humanHBVgenes                    mock   HU1016       d8
## HU1016_BD_co_D8humanHBVgenes                  coinf   HU1016       d8
##                                           replicate        sizeFactor
##                                            <factor>         <numeric>
## BD330 HBV_HDV Day 8 sample 1humanHBVgenes         c 0.859671712088571
## BD330 HBV_HDV Day 8 sample 2humanHBVgenes         d 0.882272381317184
## BD330 HBV_HDV Day 8 sample 3humanHBVgenes         e  1.26695172068585
## BD330_Ctrl_D8humanHBVgenes                          0.819509720384803
## BD330_HBV_HDV_D8_ahumanHBVgenes                   a  1.22986508958441
## ...                                             ...               ...
## Ctrl_D8_sample_1humanHBVgenes                     a  1.83841145909955
## Ctrl_D8_sample_2humanHBVgenes                     b  1.78307849410724
## Ctrl_D8_sample_3humanHBVgenes                     c  2.00991925264611
## HU1016 Ctrl D8humanHBVgenes                           0.9092752276918
## HU1016_BD_co_D8humanHBVgenes                         0.66299189294213
## 
## [[2]]
## log2 fold change (MLE): treatment coinf vs mock 
## Wald test p-value: treatment coinf vs mock 
## DataFrame with 6 rows and 12 columns
##                         baseMean    log2FoldChange             lfcSE
##                        <numeric>         <numeric>         <numeric>
## AAB59969.1      3266.14780512167  9.68708598895568 0.567064755651631
## AAB59970.1      2161.46572239315  8.84798679338145 0.748279275076424
## ENSG00000091879  174.53783945627 -2.95489654935298 0.321724994358606
## ENSG00000179776 144.822437716892 -3.26901688675925 0.368693491000597
## AAB59972.1      510.491181909056  10.6166000723435  1.21355299663552
## AAB59971.1      480.567176685875  10.5410696087127  1.24030253361156
##                              stat               pvalue
##                         <numeric>            <numeric>
## AAB59969.1       17.0828567503264 1.99126284520909e-65
## AAB59970.1       11.8244445464266 2.91826614683191e-32
## ENSG00000091879 -9.18454145983867 4.13284322757718e-20
## ENSG00000179776 -8.86648928324572 7.54882038702633e-19
## AAB59972.1        8.7483613008885 2.16473222892492e-18
## AAB59971.1       8.49878906400265  1.9157866719377e-17
##                                 padj ENTREZID SYMBOL       GENENAME
##                            <numeric>   <list> <list>         <list>
## AAB59969.1      2.95543231485933e-61       NA     NA             NA
## AAB59970.1      2.16564530756396e-28       NA     NA             NA
## ENSG00000091879 2.04465530612335e-16      285 ANGPT2 angiopoietin 2
## ENSG00000179776 2.80098980460612e-15     1003   CDH5     cadherin 5
## AAB59972.1      6.42579114834073e-15       NA     NA             NA
## AAB59971.1      4.73901763081655e-14       NA     NA             NA
##                                        ALIAS
##                                       <list>
## AAB59969.1                                NA
## AAB59970.1                                NA
## ENSG00000091879 c("AGPT2", "ANG2", "ANGPT2")
## ENSG00000179776    c("7B4", "CD144", "CDH5")
## AAB59972.1                                NA
## AAB59971.1                                NA
##                                                                                                                                      REFSEQ
##                                                                                                                                      <list>
## AAB59969.1                                                                                                                               NA
## AAB59970.1                                                                                                                               NA
## ENSG00000091879 c("NM_001118887", "NM_001118888", "NM_001147", "NP_001112359", "NP_001112360", "NP_001138", "XM_017013318", "XP_016868807")
## ENSG00000179776                 c("NM_001114117", "NM_001795", "NP_001786", "XM_011522801", "XM_024450133", "XP_011521103", "XP_024305901")
## AAB59972.1                                                                                                                               NA
## AAB59971.1                                                                                                                               NA
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ACCNUM
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  <list>
## AAB59969.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           NA
## AAB59970.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           NA
## ENSG00000091879 c("AAB63190", "AAF76526", "AAG17257", "AAI26201", "AAI26203", "AAI43903", "AAT69979", "AB009865", "AF004327", "AF187858", "AF218015", "AJ289780", "AJ289781", "AK075219", "AK225698", "AK290070", "AK310171", "AK312541", "BAA95590", "BAF82759", "BAG35440", "BC022490", "BC126200", "BC126202", "BC143902", "CAC08179", "CAC08180", "CAK96154", "DA829327", "EAW80472", "EAW80473", "EAW80474", "NM_001118887", "NM_001118888", "NM_001147", "NP_001112359", "NP_001112360", "NP_001138", "O15123", "XM_017013318", \n"XP_016868807")
## ENSG00000179776                                                                         c("AAB41796", "AAH96363", "AAH96364", "AAH96365", "AAI17521", "AB035304", "AB209908", "AK300299", "AK300322", "AK300461", "BAA87418", "BAD93145", "BAG62052", "BAG62074", "BAG62180", "BC096363", "BC096364", "BC096365", "BC117520", "BQ716387", "CAA42468", "CAA56306", "DC381809", "DC382718", "EAW83009", "NM_001114117", "NM_001795", "NP_001786", "P33151", "U84722", "X59796", "X79981", "XM_011522801", "XM_024450133", "XP_011521103", "XP_024305901")
## AAB59972.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           NA
## AAB59971.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           NA
DGE_analysis("Human d28_ctrlvcoinf")
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates

## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns

## [[1]]
## DataFrame with 16 rows and 5 columns
##                                            treatment    donor     time
##                                             <factor> <factor> <factor>
## BD330 HBV_HDV Day 28 sample 1humanHBVgenes     coinf   HU1019      d28
## BD330 HBV_HDV Day 28 sample 2humanHBVgenes     coinf   HU1019      d28
## BD330 HBV_HDV Day 28 sample 3humanHBVgenes     coinf   HU1019      d28
## BD330_Ctrl_D28humanHBVgenes                     mock   HU1019      d28
## BD330_HBV_HDV_D28_bhumanHBVgenes               coinf   HU1019      d28
## ...                                              ...      ...      ...
## Ctrl_D28_sample_1humanHBVgenes                  mock   HU1007      d28
## Ctrl_D28_sample_2humanHBVgenes                  mock   HU1007      d28
## Ctrl_D28_sample_3humanHBVgenes                  mock   HU1007      d28
## HU1016 Ctrl D28humanHBVgenes                    mock   HU1016      d28
## HU1016_BD_co_D28humanHBVgenes                  coinf   HU1016      d28
##                                            replicate        sizeFactor
##                                             <factor>         <numeric>
## BD330 HBV_HDV Day 28 sample 1humanHBVgenes         c 0.755410636651868
## BD330 HBV_HDV Day 28 sample 2humanHBVgenes         d 0.664263202368975
## BD330 HBV_HDV Day 28 sample 3humanHBVgenes         e 0.688676521272185
## BD330_Ctrl_D28humanHBVgenes                           1.20230358749222
## BD330_HBV_HDV_D28_bhumanHBVgenes                   b 0.932438545556839
## ...                                              ...               ...
## Ctrl_D28_sample_1humanHBVgenes                     a  3.71536586414676
## Ctrl_D28_sample_2humanHBVgenes                     b  3.84496101662567
## Ctrl_D28_sample_3humanHBVgenes                     c  4.26038252806512
## HU1016 Ctrl D28humanHBVgenes                         0.822938518227753
## HU1016_BD_co_D28humanHBVgenes                        0.897784791340134
## 
## [[2]]
## log2 fold change (MLE): treatment coinf vs mock 
## Wald test p-value: treatment coinf vs mock 
## DataFrame with 6 rows and 12 columns
##                         baseMean    log2FoldChange             lfcSE
##                        <numeric>         <numeric>         <numeric>
## AAB59969.1      1325.98744838806   7.8421423264979 0.577427162041115
## AAB59972.1      284.722709278814  7.31128552303804  0.68878635799948
## AAB59970.1      762.035637629851  7.47956672714904 0.739471482128307
## AAB59971.1      233.482411892535  8.15459391780692 0.937829843648784
## ENSG00000261371 314.622523632858 -2.11259427485376 0.400323405594147
## ENSG00000159189 8.59526020193391 -6.50545781928045   1.3948663152479
##                              stat               pvalue
##                         <numeric>            <numeric>
## AAB59969.1       13.5811801765216  5.1785239170969e-42
## AAB59972.1          10.6147362504 2.54512184374925e-26
## AAB59970.1       10.1147466912744 4.75244779226661e-24
## AAB59971.1       8.69517426112194 3.46297894578665e-18
## ENSG00000261371 -5.27721898178378 1.31159118616829e-07
## ENSG00000159189 -4.66385756696997 3.10336218958935e-06
##                                 padj ENTREZID SYMBOL
##                            <numeric>   <list> <list>
## AAB59969.1      1.17511064726763e-37       NA     NA
## AAB59972.1       2.8876952439179e-22       NA     NA
## AAB59970.1      3.59475151007046e-20       NA     NA
## AAB59971.1      1.96454795594476e-14       NA     NA
## ENSG00000261371 0.000595252543930618     5175 PECAM1
## ENSG00000159189   0.0117369158010269      714   C1QC
##                                                          GENENAME
##                                                            <list>
## AAB59969.1                                                     NA
## AAB59972.1                                                     NA
## AAB59970.1                                                     NA
## AAB59971.1                                                     NA
## ENSG00000261371 platelet and endothelial cell adhesion molecule 1
## ENSG00000159189                            complement C1q C chain
##                                                                                        ALIAS
##                                                                                       <list>
## AAB59969.1                                                                                NA
## AAB59972.1                                                                                NA
## AAB59970.1                                                                                NA
## AAB59971.1                                                                                NA
## ENSG00000261371 c("CD31", "CD31/EndoCAM", "GPIIA'", "PECA1", "PECAM-1", "endoCAM", "PECAM1")
## ENSG00000159189                                                   c("C1Q-C", "C1QG", "C1QC")
##                                                                                                                                                                                                                                                                                                                                                                      REFSEQ
##                                                                                                                                                                                                                                                                                                                                                                      <list>
## AAB59969.1                                                                                                                                                                                                                                                                                                                                                               NA
## AAB59972.1                                                                                                                                                                                                                                                                                                                                                               NA
## AAB59970.1                                                                                                                                                                                                                                                                                                                                                               NA
## AAB59971.1                                                                                                                                                                                                                                                                                                                                                               NA
## ENSG00000261371 c("NM_000442", "NP_000433", "XM_005276880", "XM_005276881", "XM_005276882", "XM_005276883", "XM_011524889", "XM_011524890", "XM_017024738", "XM_017024739", "XM_017024740", "XM_017024741", "XP_005276937", "XP_005276938", "XP_005276939", "XP_005276940", "XP_011523191", "XP_011523192", "XP_016880227", "XP_016880228", "XP_016880229", "XP_016880230")
## ENSG00000159189                                                                                                                                                                                                                                 c("NM_001114101", "NM_001347619", "NM_001347620", "NM_172369", "NP_001107573", "NP_001334548", "NP_001334549", "NP_758957")
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ACCNUM
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <list>
## AAB59969.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 NA
## AAB59972.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 NA
## AAB59970.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 NA
## AAB59971.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 NA
## ENSG00000261371 c("AAA36186", "AAA36429", "AAA60057", "AAB28645", "AAF91446", "AAF91447", "AAF91448", "AAF91449", "AAF91450", "AAF91451", "AAF91452", "AAF91453", "AAF91454", "AAF91455", "AAF91456", "AAF91457", "AAF91458", "AAF91459", "AAF91460", "AAH22512", "AAH51822", "AAK84009", "AAK84010", "AAK84011", "AF281287", "AF281288", "AF281289", "AF281290", "AF281291", "AF281292", "AF281293", "AF281294", "AF281295", "AF281296", "AF281297", "AF281298", "AF281299", "AF281300", "AF281301", "AF393676", "AF393677", "AF393678", \n"AFA36630", "AK091419", "AK290692", "AK303959", "AK304166", "BAF83381", "BAH14084", "BAH14122", "BC022512", "BC051822", "BC062608", "BG272085", "EAW94207", "EAW94208", "JQ287500", "M28526", "M37780", "NM_000442", "NP_000433", "P16284", "S66450", "X96849", "XM_005276880", "XM_005276881", "XM_005276882", "XM_005276883", "XM_011524889", "XM_011524890", "XM_017024738", "XM_017024739", "XM_017024740", "XM_017024741", "XP_005276937", "XP_005276938", "XP_005276939", "XP_005276940", "XP_011523191", "XP_011523192", \n"XP_016880227", "XP_016880228", "XP_016880229", "XP_016880230")
## ENSG00000159189                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             c("AAH09016", "AAP97191", "AF087892", "AK057792", "AK130613", "AK226152", "AL568589", "BAB71575", "BC009016", "BG060138", "BI824793", "CB995661", "CN480852", "DA849505", "EAW95016", "EAW95017", "EAW95018", "NM_001114101", "NM_001347619", "NM_001347620", "NM_172369", "NP_001107573", "NP_001334548", "NP_001334549", "NP_758957", "P02747")
##monoinfected cells (HBV only) versus those co-infected with HBV and HDV
DGE_analysis("Human d8_coinfvHBV")
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates

## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns

## [[1]]
## DataFrame with 16 rows and 5 columns
##                                           treatment    donor     time
##                                            <factor> <factor> <factor>
## BD330 HBV_HDV Day 8 sample 1humanHBVgenes     coinf   HU1019       d8
## BD330 HBV_HDV Day 8 sample 2humanHBVgenes     coinf   HU1019       d8
## BD330 HBV_HDV Day 8 sample 3humanHBVgenes     coinf   HU1019       d8
## BD330_HBV_D8humanHBVgenes                       HBV   HU1019       d8
## BD330_HBV_HDV_D8_ahumanHBVgenes               coinf   HU1019       d8
## ...                                             ...      ...      ...
## HBV_D8_sample_1humanHBVgenes                    HBV   HU1007       d8
## HBV_D8_sample_2humanHBVgenes                    HBV   HU1007       d8
## HBV_D8_sample_3humanHBVgenes                    HBV   HU1007       d8
## HU1016_BD_co_D8humanHBVgenes                  coinf   HU1016       d8
## HU1016_B_D8humanHBVgenes                        HBV   HU1016       d8
##                                           replicate        sizeFactor
##                                            <factor>         <numeric>
## BD330 HBV_HDV Day 8 sample 1humanHBVgenes         c 0.950093524498873
## BD330 HBV_HDV Day 8 sample 2humanHBVgenes         d 0.976852312237081
## BD330 HBV_HDV Day 8 sample 3humanHBVgenes         e  1.38937650643464
## BD330_HBV_D8humanHBVgenes                           0.800900430466113
## BD330_HBV_HDV_D8_ahumanHBVgenes                   a  1.37494189687786
## ...                                             ...               ...
## HBV_D8_sample_1humanHBVgenes                      a  1.74127401206303
## HBV_D8_sample_2humanHBVgenes                      b  1.23394211692444
## HBV_D8_sample_3humanHBVgenes                      c   1.6932244461784
## HU1016_BD_co_D8humanHBVgenes                        0.745371884953994
## HU1016_B_D8humanHBVgenes                            0.572800938373677
## 
## [[2]]
## log2 fold change (MLE): treatment coinf vs HBV 
## Wald test p-value: treatment coinf vs HBV 
## DataFrame with 6 rows and 12 columns
##                         baseMean    log2FoldChange             lfcSE
##                        <numeric>         <numeric>         <numeric>
## ENSG00000091879 65.6382271456623  -2.3627591296235 0.370286768302615
## ENSG00000145692 562.152435832317 -3.06944724615823 0.518161314324531
## ENSG00000118785 74.3419325546154 -4.35619486978631 0.746983508976083
## ENSG00000142748 61.5785594794866   -3.952728196897 0.692060351818289
## ENSG00000243955 356.677353883194 -3.20710168421617  0.56322741641844
## ENSG00000116785 337.325779177824  5.50798937099992  1.04089769578811
##                              stat               pvalue
##                         <numeric>            <numeric>
## ENSG00000091879 -6.38088998009387 1.76061765484325e-10
## ENSG00000145692 -5.92372908070053 3.14721791218355e-09
## ENSG00000118785 -5.83171491397112 5.48605924956769e-09
## ENSG00000142748 -5.71153684286606 1.11960451548743e-08
## ENSG00000243955 -5.69415051669558 1.23987670394259e-08
## ENSG00000116785  5.29157610136661 1.21266709489556e-07
##                                 padj ENTREZID SYMBOL
##                            <numeric>   <list> <list>
## ENSG00000091879 1.53050492735524e-06      285 ANGPT2
## ENSG00000145692 1.36793826553058e-05      635   BHMT
## ENSG00000118785 1.58967710188306e-05     6696   SPP1
## ENSG00000142748 2.15564963747458e-05     8547   FCN3
## ENSG00000243955 2.15564963747458e-05     2938  GSTA1
## ENSG00000116785  0.00017015944964734    10878  CFHR3
##                                                  GENENAME
##                                                    <list>
## ENSG00000091879                            angiopoietin 2
## ENSG00000145692 betaine--homocysteine S-methyltransferase
## ENSG00000118785                 secreted phosphoprotein 1
## ENSG00000142748                                 ficolin 3
## ENSG00000243955         glutathione S-transferase alpha 1
## ENSG00000116785             complement factor H related 3
##                                                                  ALIAS
##                                                                 <list>
## ENSG00000091879                           c("AGPT2", "ANG2", "ANGPT2")
## ENSG00000145692                        c("BHMT1", "HEL-S-61p", "BHMT")
## ENSG00000118785              c("BNSP", "BSPI", "ETA-1", "OPN", "SPP1")
## ENSG00000142748                             c("FCNH", "HAKA1", "FCN3")
## ENSG00000243955   c("GST-epsilon", "GST2", "GSTA1-1", "GTH1", "GSTA1")
## ENSG00000116785 c("CFHL3", "DOWN16", "FHR-3", "FHR3", "HLF4", "CFHR3")
##                                                                                                                                                                      REFSEQ
##                                                                                                                                                                      <list>
## ENSG00000091879                                 c("NM_001118887", "NM_001118888", "NM_001147", "NP_001112359", "NP_001112360", "NP_001138", "XM_017013318", "XP_016868807")
## ENSG00000145692                                                                                                                                 c("NM_001713", "NP_001704")
## ENSG00000118785 c("NM_000582", "NM_001040058", "NM_001040060", "NM_001251829", "NM_001251830", "NP_000573", "NP_001035147", "NP_001035149", "NP_001238758", "NP_001238759")
## ENSG00000142748                                                                                                       c("NM_003665", "NM_173452", "NP_003656", "NP_775628")
## ENSG00000243955                                                                 c("NM_001319059", "NM_145740", "NP_001305988", "NP_665683", "XM_005249034", "XP_005249091")
## ENSG00000116785                       c("NM_001166624", "NM_021023", "NP_001160096", "NP_066303", "XR_001736937", "XR_001736938", "XR_002958987", "XR_241062", "XR_426757")
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ACCNUM
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                <list>
## ENSG00000091879                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               c("AAB63190", "AAF76526", "AAG17257", "AAI26201", "AAI26203", "AAI43903", "AAT69979", "AB009865", "AF004327", "AF187858", "AF218015", "AJ289780", "AJ289781", "AK075219", "AK225698", "AK290070", "AK310171", "AK312541", "BAA95590", "BAF82759", "BAG35440", "BC022490", "BC126200", "BC126202", "BC143902", "CAC08179", "CAC08180", "CAK96154", "DA829327", "EAW80472", "EAW80473", "EAW80474", "NM_001118887", "NM_001118888", "NM_001147", "NP_001112359", "NP_001112360", "NP_001138", "O15123", "XM_017013318", \n"XP_016868807")
## ENSG00000145692                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           c("AAC50668", "AAD22043", "AAH12616", "AAQ90058", "ACJ13646", "AK298308", "AK303780", "AK315224", "BAG37653", "BAG60562", "BAG64739", "BC012616", "BM678994", "DA370221", "EAW95831", "EAW95832", "EU794592", "NM_001713", "NP_001704", "Q93088", "U50929")
## ENSG00000118785 c("AA665210", "AAA17675", "AAA59974", "AAA86886", "AAC28619", "AAH07016", "AAH17387", "AAH22844", "AAH93033", "AAX59003", "AAY41035", "AB209987", "AB469789", "ABI63352", "ABI63357", "ABI63358", "AEA49027", "AEA49028", "AEA49030", "AEA49031", "AF052124", "AK057738", "AK075463", "AK290090", "AK290104", "AK295491", "AK296035", "AK315461", "ALE30613", "AY956318", "BAA03554", "BAA05949", "BAA05950", "BAA05951", "BAC11635", "BAE45628", "BAF82779", "BAF82793", "BAG37848", "BAG58801", "BAH12087", "BAH58215", \n"BC007016", "BC017387", "BC022844", "BC093033", "BF699765", "BX648003", "CAA31984", "CAX69239", "CB117856", "CBX54353", "D28759", "D28760", "D28761", "DA419665", "DQ839491", "DQ846870", "DQ846871", "EAX06004", "EAX06005", "EAX06006", "EAX06007", "EAX06008", "EAX06009", "EAX06010", "HQ874460", "HQ874461", "J04765", "JF412666", "JF412667", "KR062183", "M83248", "NM_000582", "NM_001040058", "NM_001040060", "NM_001251829", "NM_001251830", "NP_000573", "NP_001035147", "NP_001035149", "NP_001238758", "NP_001238759", \n"P10451", "X13694")
## ENSG00000142748                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           c("AAH20731", "AAQ88448", "AAQ88650", "AAU85296", "AK075140", "AK309540", "AK309576", "AY358081", "AY358283", "BAC11429", "BC020731", "BG546674", "CAF86408", "CAG33089", "CR456808", "EAX07756", "EAX07757", "NM_003665", "NM_173452", "NP_003656", "NP_775628", "O75636")
## ENSG00000243955                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           c("AAA35938", "AAA36174", "AAA52615", "AAA52618", "AAA70226", "AAB20973", "AAB24012", "AAH53578", "AAI10892", "AAT06769", "AEE60991", "AK293371", "AK310324", "AL096729", "AY532928", "BAH11495", "BC053578", "BC110891", "BG430521", "BI762344", "BM973137", "CA841071", "CAG28584", "CR407656", "DC339498", "EAX04385", "HM005393", "M14777", "M15872", "M21758", "M25627", "NM_001319059", "NM_145740", "NP_001305988", "NP_665683", "P08263", "S49975", "XM_005249034", "XP_005249091")
## ENSG00000116785                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         c("AAH20687", "AAH58009", "AAH70259", "AK298459", "BAG60672", "BC020680", "BC020687", "BC058009", "BC070259", "BG618529", "CAA48639", "CBN73475", "EAW91262", "EAW91263", "EAW91264", "NM_001166624", "NM_021023", "NP_001160096", "NP_066303", "Q02985", "X68679", "XR_001736937", "XR_001736938", "XR_002958987", "XR_241062", "XR_426757")
DGE_analysis("Human d28_coinfvHBV")
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates

## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns

## [[1]]
## DataFrame with 16 rows and 5 columns
##                                            treatment    donor     time
##                                             <factor> <factor> <factor>
## BD330 HBV_HDV Day 28 sample 1humanHBVgenes     coinf   HU1019      d28
## BD330 HBV_HDV Day 28 sample 2humanHBVgenes     coinf   HU1019      d28
## BD330 HBV_HDV Day 28 sample 3humanHBVgenes     coinf   HU1019      d28
## BD330_HBV_D28humanHBVgenes                       HBV   HU1019      d28
## BD330_HBV_HDV_D28_bhumanHBVgenes               coinf   HU1019      d28
## ...                                              ...      ...      ...
## HBV_D28_sample_1humanHBVgenes                    HBV   HU1007      d28
## HBV_D28_sample_2humanHBVgenes                    HBV   HU1007      d28
## HBV_D28_sample_3humanHBVgenes                    HBV   HU1007      d28
## HU1016_BD_co_D28humanHBVgenes                  coinf   HU1016      d28
## HU1016_B_D28humanHBVgenes                        HBV   HU1016      d28
##                                            replicate        sizeFactor
##                                             <factor>         <numeric>
## BD330 HBV_HDV Day 28 sample 1humanHBVgenes         c 0.830943677633343
## BD330 HBV_HDV Day 28 sample 2humanHBVgenes         d  0.73384882041442
## BD330 HBV_HDV Day 28 sample 3humanHBVgenes         e 0.758259958349027
## BD330_HBV_D28humanHBVgenes                            2.40586075320506
## BD330_HBV_HDV_D28_bhumanHBVgenes                   b  1.03508949187203
## ...                                              ...               ...
## HBV_D28_sample_1humanHBVgenes                      a  2.24681866895274
## HBV_D28_sample_2humanHBVgenes                      b  2.97974367107981
## HBV_D28_sample_3humanHBVgenes                      c  2.34268177746246
## HU1016_BD_co_D28humanHBVgenes                        0.999170705202106
## HU1016_B_D28humanHBVgenes                            0.820750460492413
## 
## [[2]]
## log2 fold change (MLE): treatment coinf vs HBV 
## Wald test p-value: treatment coinf vs HBV 
## DataFrame with 6 rows and 12 columns
##                         baseMean    log2FoldChange             lfcSE
##                        <numeric>         <numeric>         <numeric>
## ENSG00000164181 34.1842716459638  5.96558605992868  1.20287555737347
## ENSG00000113555 15.0279506409987 -4.65455014978377  1.02594551840299
## ENSG00000107719 18.7383368186678 -4.45503264715911   1.0136228349746
## ENSG00000261371 327.705448107525 -2.00936017105432 0.453858411643614
## ENSG00000176435 16.3727700489356  -4.6449069670697  1.07724213061943
## ENSG00000110799 209.794109113549 -2.82460115213463  0.70081645400404
##                              stat               pvalue               padj
##                         <numeric>            <numeric>          <numeric>
## ENSG00000164181  4.95943742755467 7.06976145135564e-07 0.0157415308475885
## ENSG00000113555 -4.53683949711982 5.71035318194246e-06 0.0616167816305245
## ENSG00000107719 -4.39515813322294 1.10692143412422e-05 0.0616167816305245
## ENSG00000261371 -4.42728419151156 9.54269688595705e-06 0.0616167816305245
## ENSG00000176435   -4.311850451299 1.61893922716199e-05 0.0720946016639779
## ENSG00000110799  -4.0304435433794 5.56716999376128e-05  0.206597678468481
##                 ENTREZID  SYMBOL
##                   <list>  <list>
## ENSG00000164181    79993  ELOVL7
## ENSG00000113555    51294  PCDH12
## ENSG00000107719    27143   PALD1
## ENSG00000261371     5175  PECAM1
## ENSG00000176435   161198 CLEC14A
## ENSG00000110799     7450     VWF
##                                                          GENENAME
##                                                            <list>
## ENSG00000164181                       ELOVL fatty acid elongase 7
## ENSG00000113555                                  protocadherin 12
## ENSG00000107719          phosphatase domain containing, paladin 1
## ENSG00000261371 platelet and endothelial cell adhesion molecule 1
## ENSG00000176435               C-type lectin domain containing 14A
## ENSG00000110799                             von Willebrand factor
##                                                                                        ALIAS
##                                                                                       <list>
## ENSG00000164181                                                                       ELOVL7
## ENSG00000113555                                       c("VE-cadherin-2", "VECAD2", "PCDH12")
## ENSG00000107719                                               c("KIAA1274", "PALD", "PALD1")
## ENSG00000261371 c("CD31", "CD31/EndoCAM", "GPIIA'", "PECA1", "PECAM-1", "endoCAM", "PECAM1")
## ENSG00000176435                                   c("C14orf27", "CEG1", "EGFR-5", "CLEC14A")
## ENSG00000110799                                                     c("F8VWF", "VWD", "VWF")
##                                                                                                                                                                                                                                                                                                                                                                                                                                      REFSEQ
##                                                                                                                                                                                                                                                                                                                                                                                                                                      <list>
## ENSG00000164181 c("NM_001104558", "NM_001297617", "NM_001297618", "NM_024930", "NP_001098028", "NP_001284546", "NP_001284547", "NP_079206", "XM_005248606", "XM_005248607", "XM_006714695", "XM_011543651", "XM_017009885", "XM_017009886", "XM_017009887", "XM_017009888", "XM_017009889", "XP_005248663", "XP_005248664", "XP_006714758", "XP_011541953", "XP_016865374", "XP_016865375", "XP_016865376", "XP_016865377", "XP_016865378")
## ENSG00000113555                                                                                                                                                                                                                                                                                                                                                                 c("NM_016580", "NP_057664", "XM_024446106", "XP_024301874")
## ENSG00000107719                                                                                                                                                                                                                                                                    c("NM_014431", "NP_055246", "XM_011539637", "XM_011539638", "XM_017016072", "XP_011537939", "XP_011537940", "XP_016871561", "XR_001747093", "XR_945675")
## ENSG00000261371                                                                 c("NM_000442", "NP_000433", "XM_005276880", "XM_005276881", "XM_005276882", "XM_005276883", "XM_011524889", "XM_011524890", "XM_017024738", "XM_017024739", "XM_017024740", "XM_017024741", "XP_005276937", "XP_005276938", "XP_005276939", "XP_005276940", "XP_011523191", "XP_011523192", "XP_016880227", "XP_016880228", "XP_016880229", "XP_016880230")
## ENSG00000176435                                                                                                                                                                                                                                                                                                                                                                                                 c("NM_175060", "NP_778230")
## ENSG00000110799                                                                                                                                                                                                                                                                                                                                                                                                 c("NM_000552", "NP_000543")
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ACCNUM
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        <list>
## ENSG00000164181                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       c("A1L3X0", "AAI30311", "AAI30313", "AB181393", "AI769834", "AK027216", "AL137506", "BAB15697", "BAD93238", "BC094792", "BC130310", "BC130312", "BC144257", "CAB70777", "DA247166", "EAW55001", "EAW55002", "NM_001104558", "NM_001297617", "NM_001297618", "NM_024930", "NP_001098028", "NP_001284546", "NP_001284547", "NP_079206", "XM_005248606", "XM_005248607", "XM_006714695", "XM_011543651", "XM_017009885", "XM_017009886", "XM_017009887", "XM_017009888", "XM_017009889", "XP_005248663", "XP_005248664", \n"XP_006714758", "XP_011541953", "XP_016865374", "XP_016865375", "XP_016865376", "XP_016865377", "XP_016865378")
## ENSG00000113555                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     c("AAF61931", "AAF73962", "AAH42634", "AAH52973", "AAQ88794", "AB026893", "AF231025", "AF240635", "AK023785", "AK024140", "AK027282", "AK226049", "AK315029", "AY358428", "BAA95162", "BAB14677", "BAB14837", "BAB55016", "BAG37515", "BC042634", "BC052973", "CA418447", "EAW61898", "NM_016580", "NP_057664", "Q9NPG4", "XM_024446106", "XP_024301874")
## ENSG00000107719                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    c("AAI36376", "AAI36377", "AB033100", "AK021806", "BAA86588", "BC015004", "BC040163", "BC048195", "BC136375", "BC136376", "CN335744", "EAW54404", "EAW54405", "EAW54406", "NM_014431", "NP_055246", "Q9ULE6", "XM_011539637", "XM_011539638", "XM_017016072", "XP_011537939", "XP_011537940", "XP_016871561", "XR_001747093", "XR_945675")
## ENSG00000261371 c("AAA36186", "AAA36429", "AAA60057", "AAB28645", "AAF91446", "AAF91447", "AAF91448", "AAF91449", "AAF91450", "AAF91451", "AAF91452", "AAF91453", "AAF91454", "AAF91455", "AAF91456", "AAF91457", "AAF91458", "AAF91459", "AAF91460", "AAH22512", "AAH51822", "AAK84009", "AAK84010", "AAK84011", "AF281287", "AF281288", "AF281289", "AF281290", "AF281291", "AF281292", "AF281293", "AF281294", "AF281295", "AF281296", "AF281297", "AF281298", "AF281299", "AF281300", "AF281301", "AF393676", "AF393677", "AF393678", \n"AFA36630", "AK091419", "AK290692", "AK303959", "AK304166", "BAF83381", "BAH14084", "BAH14122", "BC022512", "BC051822", "BC062608", "BG272085", "EAW94207", "EAW94208", "JQ287500", "M28526", "M37780", "NM_000442", "NP_000433", "P16284", "S66450", "X96849", "XM_005276880", "XM_005276881", "XM_005276882", "XM_005276883", "XM_011524889", "XM_011524890", "XM_017024738", "XM_017024739", "XM_017024740", "XM_017024741", "XP_005276937", "XP_005276938", "XP_005276939", "XP_005276940", "XP_011523191", "XP_011523192", \n"XP_016880227", "XP_016880228", "XP_016880229", "XP_016880230")
## ENSG00000176435                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 c("AAF28963", "AAH31567", "AAQ88761", "AAS77882", "AAT92280", "AF161403", "AY358395", "AY573061", "AY606132", "BC031567", "BX248017", "BX423057", "CAD62342", "EAW65835", "NM_175060", "NP_778230", "Q86T13")
## ENSG00000110799                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 c("AAA61293", "AAA61294", "AAA61295", "AAA65940", "AAB39987", "AAB59458", "AAB59512", "AAH22258", "AEY75227", "AF086470", "AK292122", "AK297600", "AK298097", "AK301216", "AW015780", "BAF84811", "BAG59985", "BAG60382", "BAG62791", "BC022258", "BG951111", "BQ898017", "CAA26503", "CAA27765", "CAA27972", "CAA29985", "CBX54458", "CCQ25771", "CD690980", "CDI44165", "DB293903", "EAW88814", "EAW88815", "EAW88816", "EAW88817", "EAW88818", "K03028", "M10321", "M17588", "NM_000552", "NP_000543", "P04275", "U81237", \n"X02672", "X04146", "X04385")

Session Info

sessionInfo()
## R version 3.5.2 (2018-12-20)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] org.Hs.eg.db_3.6.0          AnnotationDbi_1.44.0       
##  [3] BiocInstaller_1.30.0        viridis_0.5.1              
##  [5] viridisLite_0.3.0           ggrepel_0.8.0              
##  [7] data.table_1.12.0           genefilter_1.64.0          
##  [9] RColorBrewer_1.1-2          gplots_3.0.1               
## [11] DESeq2_1.22.2               SummarizedExperiment_1.12.0
## [13] DelayedArray_0.8.0          BiocParallel_1.16.5        
## [15] matrixStats_0.54.0          Biobase_2.42.0             
## [17] GenomicRanges_1.34.0        GenomeInfoDb_1.18.1        
## [19] IRanges_2.16.0              S4Vectors_0.20.1           
## [21] BiocGenerics_0.28.0         reshape2_1.4.3             
## [23] ggplot2_3.1.0               stringr_1.3.1              
## [25] dplyr_0.7.8                
## 
## loaded via a namespace (and not attached):
##  [1] bit64_0.9-7            splines_3.5.2          gtools_3.8.1          
##  [4] Formula_1.2-3          assertthat_0.2.0       latticeExtra_0.6-28   
##  [7] blob_1.1.1             GenomeInfoDbData_1.2.0 yaml_2.2.0            
## [10] RSQLite_2.1.1          pillar_1.3.1           backports_1.1.3       
## [13] lattice_0.20-38        glue_1.3.0             digest_0.6.18         
## [16] XVector_0.22.0         checkmate_1.9.1        colorspace_1.4-0      
## [19] htmltools_0.3.6        Matrix_1.2-15          plyr_1.8.4            
## [22] XML_3.98-1.16          pkgconfig_2.0.2        zlibbioc_1.28.0       
## [25] purrr_0.2.5            xtable_1.8-3           scales_1.0.0          
## [28] gdata_2.18.0           tibble_2.0.1           htmlTable_1.13.1      
## [31] annotate_1.60.0        withr_2.1.2            nnet_7.3-12           
## [34] lazyeval_0.2.1         survival_2.43-3        magrittr_1.5          
## [37] crayon_1.3.4           memoise_1.1.0          evaluate_0.12         
## [40] foreign_0.8-71         tools_3.5.2            locfit_1.5-9.1        
## [43] munsell_0.5.0          cluster_2.0.7-1        bindrcpp_0.2.2        
## [46] compiler_3.5.2         caTools_1.17.1.1       rlang_0.3.1           
## [49] grid_3.5.2             RCurl_1.95-4.11        rstudioapi_0.9.0      
## [52] htmlwidgets_1.3        bitops_1.0-6           base64enc_0.1-3       
## [55] rmarkdown_1.11         gtable_0.2.0           DBI_1.0.0             
## [58] R6_2.3.0               gridExtra_2.3          knitr_1.21            
## [61] bit_1.1-14             bindr_0.1.1            Hmisc_4.1-1           
## [64] KernSmooth_2.23-15     stringi_1.2.4          Rcpp_1.0.0            
## [67] geneplotter_1.60.0     rpart_4.1-13           acepack_1.4.1         
## [70] tidyselect_0.2.5       xfun_0.4